[gmx-users] Re: [ atomtypes ] are not case sensitive?
I'm sorry to disturb you again. The previous questions have been solved. I delete the [ atomtypes ] description in the CO2.itp file and then the error is removed. But I have another question to ask you, can you tell me the meaning of molname, nrexcl, resnr and residue in the itp files, I read the manual, but I could not understand the directions. What is the number of CO2's nrexcl? And the other question is when running mdrun, it prompts me Fatal error: More than one settle type. Suggestion: change the least use settle constraints into 3 normal constraints. What should I do to solve this question? Thank you very much. -- View this message in context: http://gromacs.5086.n6.nabble.com/atomtypes-are-not-case-sensitive-tp4426581p461.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Re: [ atomtypes ] are not case sensitive?
On 8/5/12 12:16 PM, juanjuan0618 wrote: I'm sorry to disturb you again. The previous questions have been solved. I delete the [ atomtypes ] description in the CO2.itp file and then the error is removed. But I have another question to ask you, can you tell me the meaning of molname, nrexcl, resnr and residue in the itp files, I read the manual, but molname = molecule type name nrexcl = number of bonds that determine exclusions resnr = residue number I could not understand the directions. What is the number of CO2's nrexcl? And the other question is when running mdrun, it prompts me Fatal error: More than one settle type. Suggestion: change the least use settle constraints into 3 normal constraints. What should I do to solve this question? You're using the SETTLE algorithm for both CO2 and water. You can't do that. You should probably construct the CO2 molecule in a more robust way, i.e.: http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/vsites/index.html -Justin -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Re: [ atomtypes ] are not case sensitive?
On 1/08/2012 11:29 PM, juanjuan0618 wrote: Dear professor, Now I want to simulate the water and carbon dioxide mixture solution,but when I do the simulation with my own .gro and .itp files, I met some questions. I use gromacs4.0.7 and the water model is TIP4P2005. Q1: when I grompp the .gro( a CO2 molecular and 1240 water moleculars), .top and .mdp files, it prompts me WARNING 1 [file co2.itp, line 3]: Overriding atomtype C WARNING 2 [file co2.itp, line 4]: Overriding atomtype O how can I remove these warning？ Define them with unique names if they should be distinct, or don't redefine them if they should be the same as the ones in the force field. Q2： when I grompp the other .gro with a water cage(20 water moleculars) containing a CO2 molecular and 1240 water moleculars， it prompts me Syntax error - File co2.itp, line 1 Last line read: '[ atomtypes ]' Invalid order for directive atomtypes Can you tell me how I could remove this error? You've probably got some bizarre line ending or non-text formatting. Plain text, preferably with unix-style line endings, will work. dos2unix tool may be your friend. Thank you very much for your answers, Question 1 has been solved, but the second question is still appearing. I try to change the file style to unix by using dos2unix, but the problem isn't solved. When I change the order of the including file of the topology file, it may prompts me Syntax error - File tip4p.itp, line 4 Last line read: '[ moleculetype ]' Invalid order for directive moleculetype or prommpt me Syntax error - File co2.itp, line 1 Last line read: '[ atomtypes ]' Invalid order for directive atomtypes I can't find what's error, and I don't know how to solve the problem. Can you tell me what could I to remove this error? http://gromacs.5086.n6.nabble.com/file/n456/co2.itp co2.itp http://gromacs.5086.n6.nabble.com/file/n456/co2-01-00.top co2-01-00.top Looking forward to your reply, thank you very much. -- View this message in context: http://gromacs.5086.n6.nabble.com/atomtypes-are-not-case-sensitive-tp4426581p456.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Re: [ atomtypes ] are not case sensitive?
On 8/4/12 10:31 AM, juanjuan0618 wrote: On 1/08/2012 11:29 PM, juanjuan0618 wrote: Dear professor, Now I want to simulate the water and carbon dioxide mixture solution,but when I do the simulation with my own .gro and .itp files, I met some questions. I use gromacs4.0.7 and the water model is TIP4P2005. Q1: when I grompp the .gro( a CO2 molecular and 1240 water moleculars), .top and .mdp files, it prompts me WARNING 1 [file co2.itp, line 3]: Overriding atomtype C WARNING 2 [file co2.itp, line 4]: Overriding atomtype O how can I remove these warning？ Define them with unique names if they should be distinct, or don't redefine them if they should be the same as the ones in the force field. Q2： when I grompp the other .gro with a water cage(20 water moleculars) containing a CO2 molecular and 1240 water moleculars， it prompts me Syntax error - File co2.itp, line 1 Last line read: '[ atomtypes ]' Invalid order for directive atomtypes Can you tell me how I could remove this error? You've probably got some bizarre line ending or non-text formatting. Plain text, preferably with unix-style line endings, will work. dos2unix tool may be your friend. Thank you very much for your answers, Question 1 has been solved, but the second question is still appearing. I try to change the file style to unix by using dos2unix, but the problem isn't solved. When I change the order of the including file of the topology file, it may prompts me Syntax error - File tip4p.itp, line 4 Last line read: '[ moleculetype ]' Invalid order for directive moleculetype or prommpt me Syntax error - File co2.itp, line 1 Last line read: '[ atomtypes ]' Invalid order for directive atomtypes I can't find what's error, and I don't know how to solve the problem. Can you tell me what could I to remove this error? http://gromacs.5086.n6.nabble.com/file/n456/co2.itp co2.itp http://gromacs.5086.n6.nabble.com/file/n456/co2-01-00.top co2-01-00.top Looking forward to your reply, thank you very much. There is an order in which directives are allowed to appear. Refer to Chapter 5 of the manual. All directives at the force field level ([defaults], [atomtypes], etc) must come before any [moleculetype] can be declared. If you're moving around #include statements, you're probably breaking the required order. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Re: [ atomtypes ] are not case sensitive?
Dear professor, Now I want to simulate the water and carbon dioxide mixture solution,but when I do the simulation with my own .gro and .itp files, I met some questions. I use gromacs4.0.7 and the water model is TIP4P2005. Q1: when I grompp the .gro( a CO2 molecular and 1240 water moleculars), .top and .mdp files, it prompts me WARNING 1 [file co2.itp, line 3]: Overriding atomtype C WARNING 2 [file co2.itp, line 4]: Overriding atomtype O how can I remove these warning？ Q2： when I grompp the other .gro with a water cage(20 water moleculars) containing a CO2 molecular and 1240 water moleculars， it prompts me Syntax error - File co2.itp, line 1 Last line read: '[ atomtypes ]' Invalid order for directive atomtypes Can you tell me how I could remove this error? my co2.itp is following: [ atomtypes ] ; type masschargeptypesigma epsilon C 12.011000.5888 A 0.279180.239832 O 15.99940 -0.2944 A 0.30.687244 [ moleculetype ] ; molname nrexcl CO2 2 [ atoms ] ; nr type resnr residue atom cgnr charge mass 1 C 1CO2 C 1 0.5888 2 O 1CO2OC1 1-0.2944 3 O 1CO2OC2 1-0.2944 #ifdef FLEXIBLE [ bonds ] ; i j funct length force.c. 1 2 1 0.1163 345000.0 0.1163345000.0 1 3 1 0.1163 345000.0 0.1163345000.0 [ angles ] ; i j k funct angle force.c. 2 1 3 1 180.00 383 180.00 383 #else [ settles ] ; C funct dco doo 1 1 0.1163 0.2326 [ exclusions ] 1 2 3 2 1 3 3 1 2 #endif Looking forward to your reply, thank you very much. -- View this message in context: http://gromacs.5086.n6.nabble.com/atomtypes-are-not-case-sensitive-tp4426581p417.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Re: [ atomtypes ] are not case sensitive?
On 1/08/2012 11:29 PM, juanjuan0618 wrote: Dear professor, Now I want to simulate the water and carbon dioxide mixture solution,but when I do the simulation with my own .gro and .itp files, I met some questions. I use gromacs4.0.7 and the water model is TIP4P2005. Q1: when I grompp the .gro( a CO2 molecular and 1240 water moleculars), .top and .mdp files, it prompts me WARNING 1 [file co2.itp, line 3]: Overriding atomtype C WARNING 2 [file co2.itp, line 4]: Overriding atomtype O how can I remove these warning？ Define them with unique names if they should be distinct, or don't redefine them if they should be the same as the ones in the force field. Q2： when I grompp the other .gro with a water cage(20 water moleculars) containing a CO2 molecular and 1240 water moleculars， it prompts me Syntax error - File co2.itp, line 1 Last line read: '[ atomtypes ]' Invalid order for directive atomtypes Can you tell me how I could remove this error? You've probably got some bizarre line ending or non-text formatting. Plain text, preferably with unix-style line endings, will work. dos2unix tool may be your friend. Mark my co2.itp is following: [ atomtypes ] ; type masschargeptypesigma epsilon C 12.011000.5888 A 0.279180.239832 O 15.99940 -0.2944 A 0.30.687244 [ moleculetype ] ; molname nrexcl CO2 2 [ atoms ] ; nr type resnr residue atom cgnr charge mass 1 C 1CO2 C 1 0.5888 2 O 1CO2OC1 1-0.2944 3 O 1CO2OC2 1-0.2944 #ifdef FLEXIBLE [ bonds ] ; i j funct length force.c. 1 2 1 0.1163 345000.0 0.1163345000.0 1 3 1 0.1163 345000.0 0.1163345000.0 [ angles ] ; i j k funct angle force.c. 2 1 3 1 180.00 383 180.00 383 #else [ settles ] ; C funct dco doo 1 1 0.1163 0.2326 [ exclusions ] 1 2 3 2 1 3 3 1 2 #endif Looking forward to your reply, thank you very much. -- View this message in context: http://gromacs.5086.n6.nabble.com/atomtypes-are-not-case-sensitive-tp4426581p417.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
RE: [gmx-users] Re: [ atomtypes ] are not case sensitive?
Yes. I changed this, since it is required for Amber support with proper atom type names. But I seem to have forgotten to add it to the 4.5 release notes. Berk From: awil...@ebi.ac.uk Date: Thu, 6 Jan 2011 10:23:25 + To: gmx-users@gromacs.org CC: Subject: [gmx-users] Re: [ atomtypes ] are not case sensitive? Dear GMX list, It's more the 2 years ago and now with my gmx.top file containing: [ atomtypes ];name bond_type mass charge ptype sigma epsilon Amb CA CA 0.0 0.0 A 3.39967e-01 3.59824e-01 ; 1.91 0.0860 caca 0. 0. A 3.39967e-01 3.59824e-01 And using GMX 4.5 and I don't see this complain anymore: WARNING 1 [file system_GMX.top, line 43]: Overriding atomtype CA Should I assume that gromacs finally made its atomtypes case sensitive? Only version 4.5 and above? Many thanks, Alan On 21 August 2008 09:07, Alan alanwil...@gmail.com wrote: Well, I didn't developed Amber FF neither GAFF and although only Amber FF is ported to GMX, one of the greatest appealing of Amber is its antechamber and GAFF for generating topology for non usual compounds. Looking at the way GAFF was developed (remember G is for generalised) is seemed a natural step to me to use the same name for atom types but using a different cases. So have said that, I did a look at my converted topology file by amb2gmx/acpypi and found that, although for vdw parameters they seem the same, this doesn't hold for bonds for example. I have this in my GMX top file: [ bonds ]...96 97 11.0800e-013.0711e+05 ;CZ2 - HZ2 (AT CA - HA) Protein ...3154 3194 11.0870e-012.8811e+05 ;C76 - H76 (AT ca - ha) Ligand Anyway, after all this discussion, I realized (correct if I am wrong please) that as long as the vdw parameters are the same, anything else is NOT affected because even for the example of bonds above atom types change nothing since parameters are explicit. Then, I decided to compare gaff.dat and parm99.dat (topology parameters files for Amber package) for vdw. I did found 2 atom types with same name (diff case though) and diff parameters: parm99.dat HP 1.1000 0.0157 Veenstra et al JCC,8,(1992),963 Na 1.8680 0.00277Na+ Aqvist JPC 1990,94,8021. (adapted) gaff.dat hp 0.6000 0.0157 same to hs (be careful !) na 1.8240 0.1700 OPLS Observe by the comments (4th column) that although they have the same name (but diff by case) they are completely unrelated, hence the diff values for r0 and epsilon. So, in the end, at least for example gaff.dat x parm99.dat (note that Amber has several others parm*.dat and glycam*.dat), I do have a conflicting case issue that would affect my topology in GMX format if using amb2gmx/acpypi tool for conversion. Pondering a bit more, I came to the conclusion that at least for acpypi (which I am developing), I can make it aware of this conflicting atom type naming issue and rename it when converting from Amber to GMX. About changing something in GMX? Frankly I don't know, but I hope that this thread can be of some use for someone else who stumbles in this problem. Cheers and many thanks for attention dear Berk. Alan From: Berk Hess g...@hotmail.com Subject: RE: [gmx-users] RE: [ atomtypes ] are not case sensitive? Hi, I don't know if any thinking went into the (non) case specifity of atom types. Nearly all string comparisons in Gromacs are not case specific. For things like atom names this makes sense. We could change the atom type comparisons to case specific. I think that all force field files supplied with Gromacs have consistent cases. But some users might have made force fields where this would cause problems. I think it is bad practice to distinguish atom types just by case, this makes things quite error prone. But allowing this probably does not mean that many people would do this. Another option would be to add an option to grompp. Berk. Date: Tue, 19 Aug 2008 12:03:57 +0100 From: alanwil...@gmail.com To: gmx-users@gromacs.org Subject: [gmx-users] RE: [ atomtypes ] are not case sensitive? Dear Berk, Thanks for your attention. I don't know how familiar are you to amb2gmx and ffamber port to GMX. I am just learning since I am trying to test an application that is related to amb2gmx and ffamber (acpypi). So, for Amber MD (MD to contrast with FF), Generalised Amber Force Field (GAFF) uses all the atom types (AT) usually defined for Amber FF and several more AT but in lower case. I cannot assure 100% but I believe that for all common AT (being upper or lower), they share the same parameters including when found in bonds, angles etc. parameters. If so, then, it's not a problem if GMX is not sensitive about AT lower or upper case, because in the end they are the same. But, as I said
[gmx-users] Re: [ atomtypes ] are not case sensitive?
Dear GMX list, It's more the 2 years ago and now with my gmx.top file containing: [ atomtypes ] ;name bond_type mass charge ptype sigma epsilon Amb CA CA 0.0 0.0 A 3.39967e-01 3.59824e-01 ; 1.91 0.0860 caca 0. 0. A 3.39967e-01 3.59824e-01 And using GMX 4.5 and I don't see this complain anymore: WARNING 1 [file system_GMX.top, line 43]: Overriding atomtype CA Should I assume that gromacs finally made its atomtypes case sensitive? Only version 4.5 and above? Many thanks, Alan On 21 August 2008 09:07, Alan alanwil...@gmail.com wrote: Well, I didn't developed Amber FF neither GAFF and although only Amber FF is ported to GMX, one of the greatest appealing of Amber is its antechamber and GAFF for generating topology for non usual compounds. Looking at the way GAFF was developed (remember G is for generalised) is seemed a natural step to me to use the same name for atom types but using a different cases. So have said that, I did a look at my converted topology file by amb2gmx/acpypi and found that, although for vdw parameters they seem the same, this doesn't hold for bonds for example. I have this in my GMX top file: [ bonds ] ... 96 97 11.0800e-013.0711e+05 ;CZ2 - HZ2 (AT CA - HA) Protein ... 3154 3194 11.0870e-012.8811e+05 ;C76 - H76 (AT ca - ha) Ligand Anyway, after all this discussion, I realized (correct if I am wrong please) that as long as the vdw parameters are the same, anything else is NOT affected because even for the example of bonds above atom types change nothing since parameters are explicit. Then, I decided to compare gaff.dat and parm99.dat (topology parameters files for Amber package) for vdw. I did found 2 atom types with same name (diff case though) and diff parameters: parm99.dat HP 1.1000 0.0157 Veenstra et al JCC,8,(1992),963 Na 1.8680 0.00277Na+ Aqvist JPC 1990,94,8021. (adapted) gaff.dat hp 0.6000 0.0157 same to hs (be careful !) na 1.8240 0.1700 OPLS Observe by the comments (4th column) that although they have the same name (but diff by case) they are completely unrelated, hence the diff values for r0 and epsilon. So, in the end, at least for example gaff.dat x parm99.dat (note that Amber has several others parm*.dat and glycam*.dat), I do have a conflicting case issue that would affect my topology in GMX format if using amb2gmx/acpypi tool for conversion. Pondering a bit more, I came to the conclusion that at least for acpypi (which I am developing), I can make it aware of this conflicting atom type naming issue and rename it when converting from Amber to GMX. About changing something in GMX? Frankly I don't know, but I hope that this thread can be of some use for someone else who stumbles in this problem. Cheers and many thanks for attention dear Berk. Alan From: Berk Hess g...@hotmail.com Subject: RE: [gmx-users] RE: [ atomtypes ] are not case sensitive? Hi, I don't know if any thinking went into the (non) case specifity of atom types. Nearly all string comparisons in Gromacs are not case specific. For things like atom names this makes sense. We could change the atom type comparisons to case specific. I think that all force field files supplied with Gromacs have consistent cases. But some users might have made force fields where this would cause problems. I think it is bad practice to distinguish atom types just by case, this makes things quite error prone. But allowing this probably does not mean that many people would do this. Another option would be to add an option to grompp. Berk. Date: Tue, 19 Aug 2008 12:03:57 +0100 From: alanwil...@gmail.com To: gmx-users@gromacs.org Subject: [gmx-users] RE: [ atomtypes ] are not case sensitive? Dear Berk, Thanks for your attention. I don't know how familiar are you to amb2gmx and ffamber port to GMX. I am just learning since I am trying to test an application that is related to amb2gmx and ffamber (acpypi). So, for Amber MD (MD to contrast with FF), Generalised Amber Force Field (GAFF) uses all the atom types (AT) usually defined for Amber FF and several more AT but in lower case. I cannot assure 100% but I believe that for all common AT (being upper or lower), they share the same parameters including when found in bonds, angles etc. parameters. If so, then, it's not a problem if GMX is not sensitive about AT lower or upper case, because in the end they are the same. But, as I said before, I am not 100% sure about it. However, for Amber MD, case matters! Anyway, I am just worried about integrating Amber FF in GMX. If using ffamber port this problem doesn't appear because for Amber FF (ffamber*.itp files in GMX/top folder), AT are defined as, e.g., 'amber99_27', and so if I add a ligand.itp build
[gmx-users] RE: [ atomtypes ] are not case sensitive?
Dear Berk, Thanks for your attention. I don't know how familiar are you to amb2gmx and ffamber port to GMX. I am just learning since I am trying to test an application that is related to amb2gmx and ffamber (acpypi). So, for Amber MD (MD to contrast with FF), Generalised Amber Force Field (GAFF) uses all the atom types (AT) usually defined for Amber FF and several more AT but in lower case. I cannot assure 100% but I believe that for all common AT (being upper or lower), they share the same parameters including when found in bonds, angles etc. parameters. If so, then, it's not a problem if GMX is not sensitive about AT lower or upper case, because in the end they are the same. But, as I said before, I am not 100% sure about it. However, for Amber MD, case matters! Anyway, I am just worried about integrating Amber FF in GMX. If using ffamber port this problem doesn't appear because for Amber FF (ffamber*.itp files in GMX/top folder), AT are defined as, e.g., 'amber99_27', and so if I add a ligand.itp build with help of antechamber with GAFF to my system, the AT types will never conflict with ffamber*.itp. So, to summarise, I am really concerned that GMX is not case sensitive in the matter of AT. Is there any special reason for doing so? From: Berk Hess [EMAIL PROTECTED] In this case at least the non-bonded parameters seem to be the identical. Are there some different parameters for atom types which only differ in case? Hence, I don't have a clear example to answer your question, but I am investigating. Cheers, Alan That is bad practice IMHO. But if so, we should consider changing this or adding an option. Berk. Date: Thu, 14 Aug 2008 14:41:06 +0100 From: [EMAIL PROTECTED] To: gmx-users@gromacs.org Subject: [gmx-users] [ atomtypes ] are not case sensitive? Dears, Playing with amb2gmx.pl, I have in my topol.top file something like: [snip] CC 0.0 0.0 A 3.39967e-01 3.59824e-01 ; 1.91 0.0860 ... cc 0.0 0.0 A 3.39967e-01 3.59824e-01 ; 1.91 0.0860[snip] Then, running grompp, I got several warnings, e.g.: WARNING 1 [file multi_GMX.top, line 38]: Overriding atomtype c... Is there any special reason why atomtypes are not case sensitive? Fortunately it seems that all lower case atomtypes from gaff.dat (GAFF) mirrors the upper case of, say, parm99.dat (AMBER 99). But this is not good in MHO. Many thanks in advance. Cheers,Alan -- Alan Wilter S. da Silva, D.Sc. - CCPN Research Associate Department of Biochemistry, University of Cambridge. 80 Tennis Court Road, Cambridge CB2 1GA, UK. http://www.bio.cam.ac.uk/~awd28 ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
RE: [gmx-users] RE: [ atomtypes ] are not case sensitive?
Hi, I don't know if any thinking went into the (non) case specifity of atom types. Nearly all string comparisons in Gromacs are not case specific. For things like atom names this makes sense. We could change the atom type comparisons to case specific. I think that all force field files supplied with Gromacs have consistent cases. But some users might have made force fields where this would cause problems. I think it is bad practice to distinguish atom types just by case, this makes things quite error prone. But allowing this probably does not mean that many people would do this. Another option would be to add an option to grompp. Berk. Date: Tue, 19 Aug 2008 12:03:57 +0100 From: [EMAIL PROTECTED] To: gmx-users@gromacs.org Subject: [gmx-users] RE: [ atomtypes ] are not case sensitive? Dear Berk, Thanks for your attention. I don't know how familiar are you to amb2gmx and ffamber port to GMX. I am just learning since I am trying to test an application that is related to amb2gmx and ffamber (acpypi). So, for Amber MD (MD to contrast with FF), Generalised Amber Force Field (GAFF) uses all the atom types (AT) usually defined for Amber FF and several more AT but in lower case. I cannot assure 100% but I believe that for all common AT (being upper or lower), they share the same parameters including when found in bonds, angles etc. parameters. If so, then, it's not a problem if GMX is not sensitive about AT lower or upper case, because in the end they are the same. But, as I said before, I am not 100% sure about it. However, for Amber MD, case matters! Anyway, I am just worried about integrating Amber FF in GMX. If using ffamber port this problem doesn't appear because for Amber FF (ffamber*.itp files in GMX/top folder), AT are defined as, e.g., 'amber99_27', and so if I add a ligand.itp build with help of antechamber with GAFF to my system, the AT types will never conflict with ffamber*.itp. So, to summarise, I am really concerned that GMX is not case sensitive in the matter of AT. Is there any special reason for doing so? From: Berk Hess [EMAIL PROTECTED] In this case at least the non-bonded parameters seem to be the identical. Are there some different parameters for atom types which only differ in case? Hence, I don't have a clear example to answer your question, but I am investigating. Cheers,Alan That is bad practice IMHO. But if so, we should consider changing this or adding an option. Berk. Date: Thu, 14 Aug 2008 14:41:06 +0100 From: [EMAIL PROTECTED] To: gmx-users@gromacs.org Subject: [gmx-users] [ atomtypes ] are not case sensitive? Dears, Playing with amb2gmx.pl, I have in my topol.top file something like: [snip] CC 0.0 0.0 A 3.39967e-01 3.59824e-01 ; 1.91 0.0860 ... cc 0.0 0.0 A 3.39967e-01 3.59824e-01 ; 1.91 0.0860[snip] Then, running grompp, I got several warnings, e.g.: WARNING 1 [file multi_GMX.top, line 38]: Overriding atomtype c... Is there any special reason why atomtypes are not case sensitive? Fortunately it seems that all lower case atomtypes from gaff.dat (GAFF) mirrors the upper case of, say, parm99.dat (AMBER 99). But this is not good in MHO. Many thanks in advance. Cheers,Alan -- Alan Wilter S. da Silva, D.Sc. - CCPN Research Associate Department of Biochemistry, University of Cambridge. 80 Tennis Court Road, Cambridge CB2 1GA, UK. http://www.bio.cam.ac.uk/~awd28 _ Express yourself instantly with MSN Messenger! Download today it's FREE! http://messenger.msn.click-url.com/go/onm00200471ave/direct/01/___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
